tbuckley/cabot-search huggingface dataset:
Abstract 76: Reprogramming of the preinvasive breast microenvironment identified by spatial nucleus barcoding
Authors: Kaile Wang, Zhenna Xiao, Yiyun Lin, Runmin Wei, Jie Ye, Rui Ye, Min Hu, Shanshan Bai, Emi Sei, Aatish Thennavan, Bora Lim, Andrew Futreal, Alastair Thompson, Savitri Krishnamurthy, Nicholas Navin
Journal: Cancer Research (2023)

Abstract Ductal-carcinoma-in-situ (DCIS) is the most common early-stage breast cancer and a non-obligate precursor to invasive breast cancer. However our understanding of the spatial microenvironment and the reprogramming of cell types in DCIS remains limited. To address this question, we developed a Spatial Nucleus Barcoding (SNuBar) method that utilizes a single oligonucleotide adaptor to preserve spatial information followed by performing single nucleus RNA sequencing. We validated the accuracy and scalability of SNuBar in cell lines and applied this method to investigate the spatial microenvironment of 4 normal breast tissues, 7 normal adjacent DCIS tissues, and 8 DCIS cancers. The analysis of single cells isolated from 596 macrodissected spatial regions identified 13 major cell types and 43 cell states, that co-localized in different combinations across four main topographic areas. Spatial analysis revealed that vascular and myoepithelial cells were reprogrammed in localized zones near the premalignant cells, while fibroblasts, T-cells and myeloid cells were reprogrammed across broader fields. Our data shows that many diverse cell types are reprogrammed in spatially-defined areas in the DCIS microenvironment, relative to the normal breast tissue regions. Citation Format: Kaile Wang, Zhenna Xiao, Yiyun Lin, Runmin Wei, Jie Ye, Rui Ye, Min Hu, Shanshan Bai, Emi Sei, Aatish Thennavan, Bora Lim, Andrew Futreal, Alastair Thompson, Savitri Krishnamurthy, Nicholas Navin. Reprogramming of the preinvasive breast microenvironment identified by spatial nucleus barcoding [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 76.
Abstract 4004: Targeting drug-resistant acute myeloid leukemia (AML) cells using novel casein kinase II (CK2) inhibitor
Authors: Koby Duke, Katherine Mercer, Rajesh Rajaiah, Muhammad Daniyal, Yi Qiu, Ashok Purandare, Yasin Uzun, Lijun Zhang, Morgann Klink, Chandrika Gowda
Journal: Cancer Research (2023)

Abstract Introduction: Protein Kinase CK2 level and activity are high in Acute Myeloid Leukemia (AML) stem cells. Genetic inhibition of CK2 promotes apoptosis and shows synergistic cytotoxic activity with cytotoxic therapy. Here we report the anti-leukemia efficacy of a novel and potent small molecule inhibitor of CK2, BMS-135, in AML mouse models. Methods: AML cell lines (n=8) and primary AML cells (n=3) representing various AML genetic subtypes (MLL rearranged, FLT3-ITD, TP53 mutation) were tested in vitro. Cells were treated with serial dilution of BMS-135 for 24 to 48hrs, and cell viability was measured using calorimetric cell viability (WST) assay. Similarly, treated cells were analyzed for cell cycle distribution, apoptosis, and colony formation. We measured the mRNA and protein levels of known CK2 targets. RNA sequencing and gene expression analysis was done to evaluate gene expression changes following treatment with BMS-135. Cell line-derived xenograft and patient-derived xenograft of AML were treated with BMS-135 at a dose of 7.5mg/kg oral gavage twice daily for 21 days or vehicle. Results: Combined in vitro and in vivo experiments establish the efficacy of BMS-135. Cytotoxicity at inhibitory concentrations of 30-800nM, G0-G1 cell cycle arrest, increased apoptosis, and poor colony formation following treatment were noted consistently in all cells. Single-drug treatment with BMS-135 achieved 50-80% leukemia inhibition and significantly prolonged survival in treated mice after 3 weeks of therapy. Following in vivo treatment with BMS-135, we confirmed the inhibition of known CK2 targets (AKT, PI3K, Bcl-xL) in the bone marrow and spleen AML cells. No significant myelosuppression or organ toxicity was noted in tumor-bearing mice following 3 weeks of treatment when compared to vehicle-treated mice. BMS-135 shows synergistic cytotoxic activity with daunorubicin and cytarabine. Conclusions: Selective inhibitor of CK2 is well tolerated and shows superior in vivo efficacy and target inhibition in a series of AML cells and xenografts. BMS-135 works synergistically with cytotoxic agents like daunorubicin and cytarabine. These results support further pre-clinical characterization and clinical development of BMS-135 for treating AML in combination with cytotoxic therapy. Citation Format: Koby Duke, Katherine Mercer, Rajesh Rajaiah, Muhammad Daniyal, Yi Qiu, Ashok Purandare, Yasin Uzun, Lijun Zhang, Morgann Klink, Chandrika Gowda. Targeting drug-resistant acute myeloid leukemia (AML) cells using novel casein kinase II (CK2) inhibitor. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4004.
Abstract 1898: Racial/ethnic disparities in stage at diagnosis among women with cervical cancer in Texas: Mediating effects of neighborhood-level socioeconomic deprivation
Authors: Itunu O. Sokale, Abiodun O. Oluyomi, Aaron P. Thrift
Journal: Cancer Research (2023)

Abstract Background: Although mortality from cervical cancer has declined steadily in the U.S. since the advent of population-based screening in the 1970s, the benefit has not reached all racial/ethnic groups of patients equally. This study examined the underlying role of neighborhood-level socioeconomic disadvantage as a potential mediator of the association between race/ethnicity and being diagnosed with late-stage versus early-stage cervical cancer. Methods: We analyzed Texas Cancer Registry data for cervical cancer cases diagnosed among women aged 18 or older from 2010 to 2018. Cervical cancer cases were categorized as early or late stage at diagnosis. First, we used a stepwise hierarchical logistic regression model to examine the associations between race/ethnicity and stage at diagnosis. Then, we performed causal mediation analyses using the counterfactual framework approach to estimate the direct, indirect (mediated), and total effects, and percent mediated. Results: Of the 9525 women with cervical cancer, 4869 (2200 non-Hispanic White (NHW) (45.2%), 720 non-Hispanic Black (NHB) (14.8%), 1800 Hispanic (37.0%)) had late-stage cervical cancer at diagnosis (overall, 51.1%). Women 65 years or older, NHB, Hispanic, with Medicaid/Medicare, uninsured, and those who reside in more deprived neighborhoods were more likely to present with advanced cervical cancer at diagnosis (p &amp;lt;0.001). Compared to NHW women (11.8%), NHB (28.5%) and Hispanic (34.4%) women were more likely to live in most deprived neighborhoods and had greater odds of late-stage cervical cancer diagnosis (unadjusted odds ratios 1.49 (95% CI 1.31-1.69) and 1.20 (95% CI 1.10-1.31), respectively). In the age-adjusted mediation analysis, 23.1% and 52.2% of the disparity were attributable to higher disadvantages among NHB and Hispanic women, respectively.Conclusions: Results of mediation analyses suggested that area-level deprivation explained some of the racial/ethnic disparities in stage at diagnosis of cervical cancer among NHB and Hispanic women versus NHW women.Impact: These findings can be applied to develop targeted and race-specific interventions to improve early diagnosis and treatment of cervical cancer for cancer care equity. Citation Format: Itunu O. Sokale, Abiodun O. Oluyomi, Aaron P. Thrift. Racial/ethnic disparities in stage at diagnosis among women with cervical cancer in Texas: Mediating effects of neighborhood-level socioeconomic deprivation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1898.
Abstract 5495: Combination therapy with poly (ADP-ribose) polymerase inhibitor in endometrial cancer
Authors: Conway Xu, Xiaonan Hou, Erik Jessen, Chen Wang, S. John Weroha
Journal: Cancer Research (2023)

Abstract Objective: Endometrial cancer (EC) is the most common gynecologic malignancy and serous histology is the second most common subtype. It is associated with poorer outcomes as recurrent disease tends to be resistant to chemotherapy. Given the dearth of proven targeted therapies in this setting and the tendency for serous ECs to have homologous recombination deficiency (HRD), this study aimed to test the synergy between poly (ADP-ribose) polymerase inhibitors (PARPis) and SN38, an active metabolite of DNA topoisomerase I, irinotecan. PARPis are currently FDA approved in ovarian cancer and have their greatest efficacy in tumors with HRD while topoisomerase inhibitors are a standard chemotherapy option for recurrent cancer. Methods: A genomic instability score (GIS) was derived from low-pass whole genome sequencing-based bioinformatics analysis according to three previously reported HRD metrics: telomeric allelic imbalance, large state transitions, and loss of heterozygosity. GIS was calculated for 34 patient derived xenograft (PDX) tumors, of which eight had serous histology. PARPi, rucaparib, and SN38 were used to treat EC PDX tumors in ex vivo 3D cell culture experiments using RealTime Glo for viability after 4-5 days of drug exposure. Synergy was assessed by calculating the combination index (CI) using Chou-Talalay method. Results: GIS ≥ 42 was noted in 62.5% (5/8) of serous EC PDX tumors and only 19.2% (5/26) of non-serous EC PDX tumors. Synergy (CI &amp;lt; 1.0) between rucaparib and SN38 was demonstrated in 85.7% (6/7) of serous EC PDX ex vivo 3D cell culture experiments, but only 62.5% (10/16) of non-serous EC PDX tumors. Conclusions: Most serous EC PDX tumors had a high GIS, consistent with HRD, when compared to a minority of non-serous histologies. Furthermore, combination therapy of rucaparib and SN38 had a synergistic effect in almost all serous EC PDX models, while still being effective in a majority of non-serous models. Additional PDX tumors need to be assessed to establish the predictive value of a GIS on synergy between rucaparib and SN38. Further in vivo studies are also needed to confirm these ex vivo findings of synergy. Ultimately, the hope is to generate preclinical data which justifies the use of PARPis in serous ECs as monotherapy or in combination with other anticancer therapies. Citation Format: Conway Xu, Xiaonan Hou, Erik Jessen, Chen Wang, S. John Weroha. Combination therapy with poly (ADP-ribose) polymerase inhibitor in endometrial cancer. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5495.
Abstract 2183: Absolute quantification of PD-L1 gene expression in single cell on tissue for accurately predicting response to ICIs
Authors: Amandine Gerstenberg, Adele Ponzoni, Corinne Ramos, Jonathan Stauber
Journal: Cancer Research (2023)

Abstract Background PD-L1 immunohistochemistry (IHC) has been traditionally used for predicting clinical responses to immune checkpoint inhibitors (ICIs). However, there are at least 4 different assays and antibodies used for PD-L1 IHC, each developed with a different ICI. Spatial transcriptomic analysis at the single cell level can be helpful for deeply characterize the complexity and heterogeneity of tumors. We set to test if in-situ hybridization-based RNA scope coupled to single cell quantification is a robust method to determine PD-L1 mRNA expression levels in each cell and furthermore efficacy of predicting response to ICIs as compared to routinely used standardized IHC procedures. Method FFPE sections from retrospectively collected surgically resected NSCLCs (adenocarcinoma and squamous cell carcinoma) tumor with progression disease or complete response from adjuvant pembrolizumab therapy were used. Target genes CD274 (PD-L1) and GZMB (Granzyme B) were assessed. For fluorescent detection, the label probe was conjugated to Opal 570 and 620 respectively. Tissues cells were counterstained with DAPI to detect the nuclei. A Digital pathology software QuPath was used for cell segmentation and dot’s detection for gene expression quantification and further classification. Results Difference in expression levels were seen between PD-L1 and GZMB across the tumor with PD-L1 staining mostly located in the tumoral area and Granzyme B in stromal area of the NSCLC tissue. This is consistent with the expected expression of PD-L1 on tumor epithelial cells and Granzyme B on T cells. This heterogeneity in the signal distribution specific to the analyzed tissue correspond to intra-tissue cells metabolism heterogeneity between cell types. This heterogeneity of expression was captured though a digital workflow capable of quantifying the number of cells expressing PD-L1 and GZMB. Among the cells expressing the markers, 96% were positive for PD-L1 for the tumor that did not respond to therapy with the threshold of positivity being set at 1 of dots, that corresponds to 1 transcript, per cell. Conclusion Our results demonstrate that PD-L1 was highly expressed in a tumor context that was not responding to PD-1 ICI inhibitor. Measurement of mRNA expression at the single cell level on tissue provides another layer of PD-L1 detection which can be exploited to predict tumor response to ICI suggesting that moving forward with this technology is a viable approach for this dynamic biomarker. Citation Format: Amandine Gerstenberg, Adele Ponzoni, Corinne Ramos, Jonathan Stauber. Absolute quantification of PD-L1 gene expression in single cell on tissue for accurately predicting response to ICIs [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2183.
Abstract 3274: Novel cell-based bioassays for mono- and multi-specific antibodies targeting PD-1/PD-L1 for combination immunotherapy
Authors: Jun Wang, Julia Gilden, Denise Garvin, Pete Stecha, Jim Hartnett, Frank Fan, Mei Cong, Jamison Grailer
Journal: Cancer Research (2023)

Abstract Programmed cell death protein 1 (PD-1) is an immune checkpoint (IC) receptor that negatively regulates T cell function. Blocking the interaction of PD-1 with its ligands PD-L1 or PD-L2 unleashes the immune system and enhances anti-tumor responses. Immunotherapy using PD-1 or PD-L1 blocking antibodies has led to a paradigm shift in cancer drug discovery, due to its durable effect against a wide variety of cancers. However, despite its tremendous clinical success in cancer treatment, a significant fraction of patients and tumor types remain unresponsive to this therapy. This has led to the development of combination therapies linking PD-1 checkpoint inhibitors with inhibitors of several other IC receptors. A major challenge in immunotherapy drug development is the lack of quantitative and reproducible functional assays. Existing methods rely heavily on primary immune cells are highly variable and labor-intensive. Here, we report the development of a suite of cell line-based reporter bioassays for monoclonal antibodies targeting human PD-1/PD-L1, or bispecific antibodies targeting PD-1/PD-L1 and a co-stimulatory receptor (e.g., 4-1BB, OX40, ICOS) or an immune inhibitory receptor (e.g., CTLA-4, LAG-3, TIGIT). A mouse PD-1/PD-L1 assay and a human PD-1/PD-L2 assay are also developed and can be used in parallel with human PD-1/PD-L1 assay to enable preclinical studies and assess assay specificity. Each of these assays consist of two engineered cell lines: a T effector cell line that express a luciferase reporter driven by specific promoter/response elements responding to the intracellular signals mediated by the T cell receptor (TCR), with modulation from PD-1 and the second immune receptor, and an engineered artificial antigen presenting cell (aAPC). Importantly, these combination bioassays demonstrate the synergetic effect of PD-1 blockade with blockade of a second IC inhibitor receptor or activation of a costimulatory receptor, thus reflecting the mechanisms of action for the therapeutic antibodies of interest. The bioassays are sensitive and quantitative, are prequalified according to ICH guidelines, and demonstrate the performance characteristics (specificity, precision, accuracy, and linearity) to be used as potency assays for product release and stability studies during immunotherapy drug development. Citation Format: Jun Wang, Julia Gilden, Denise Garvin, Pete Stecha, Jim Hartnett, Frank Fan, Mei Cong, Jamison Grailer. Novel cell-based bioassays for mono- and multi-specific antibodies targeting PD-1/PD-L1 for combination immunotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3274.
Abstract 1918: Reducing human papillomavirus associated cancers and disparities among Hispanics/Latinos through the adapted NCI NON CHE (National Outreach Network Community Health Education) program
Authors: Alejandra Ramos, Carolina Aristizabal, Lourdes Baezconde-Garbanati
Journal: Cancer Research (2023)

Abstract While HPV vaccination has dramatically reduced HPV-related cancer incidences in certain demographic groups, it continues to disproportionately affect Hispanics/Latinos. The NON CHE program at (USC), (NCCC), aims to understand the gaps in Human Papillomavirus (HPV) knowledge and vaccination uptake, cervical cancer screenings, and addresses the barriers to participating in clinical trials (CT) by conducting culturally-sensitive educational workshops to the community. Methods: Materials such as a PowerPoint presentation and Human Papillomavirus Vaccination (HPV) infographics were adapted by the NCI to ensure the message can influence the target audience. Educational workshops were conducted via Zoom. Recruitment of participants were facilitated by partnering with community organizations across Los Angeles County (LAC) which is NCCC’s catchment area. The effectiveness of the workshops was assessed by delivery of pre and post surveys that captured demographics and a series of true and false questions that measured HPV knowledge. 3- and 6-month follow-up surveys are distributed among participants of those of age 18 - 26 and to parents of children 9 - 18 years of age to assess vaccination intake. Results: A total of 1,515 people have been reached during educational workshops, health fairs, and outreach events from October 2021 to September 2022. Our results demonstrate that the 236 participants, (55.6%) Spanish-speaking and (26.9%) English-speaking had not heard of HPV indicating the sparse availability and accessibility of information contributing to parents’ unfamiliarity of the HPV vaccine (79.5%) between the two groups. However, there was a positive distribution of likely to get vaccine (72.88%) and likely to vaccinate their children (47.88%.) Their lack of awareness stemmed from lack of provider motivation (44.2%) and limited health education (39.5%.) Conclusion: Conducting culturally tailored educational workshops to disseminate information on Human Papillomavirus (HPV) has helped Hispanics/Latinos understand what HPV is and reduce the stigma. Effective dissemination of HPV education requires it to be inclusive, concise, and engaging to motivate community members to seek preventive care. Citation Format: Alejandra Ramos, Carolina Aristizabal, Lourdes Baezconde-Garbanati. Reducing human papillomavirus associated cancers and disparities among Hispanics/Latinos through the adapted NCI NON CHE (National Outreach Network Community Health Education) program [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1918.
Abstract 3106: Design, synthesis, and screening of niclosamide analogs as androgen receptor degraders for hepatocellular carcinoma
Authors: Jeffrey Cheng, Enming Xing, Shabber Mohammed, Emma Montgomery, Lauren Granchie, Christopher Coss, Pui-Kai Li
Journal: Cancer Research (2023)

Abstract Hepatocellular Carcinoma (HCC) is the leading form of liver cancer, the 6th most common type, and the 4th leading cause of cancer death worldwide. Interestingly, HCC occurs two to four times more in males than females. A possible explanation for this sexual dimorphism is the implication of androgen and the Androgen Receptor (AR). However, previous clinical trials among HCC patients have shown no significant survival benefit after the administration of antiandrogen drugs (e.g. Enzalutamide) that block the Ligand-Binding Domain (LBD) of the Full-length Androgen Receptor (AR-FL). Instead, our lab has developed a novel approach using small molecular analogs of the previously FDA-approved drug, Niclosamide, to degrade full-length AR and its spliced variants within HCC cell lines. The primary goal of this project was to evaluate the minimal necessary pharmacophores for the biological activity of the Niclosamide scaffold. To do so, 23 analogs were synthesized and tested on three different HCC cell lines (SNU 475, 423, and LM3) using a CCK8 cell viability assay. Preliminary results have shown that only Niclosamide analogs with i.) electron-withdrawing groups on the aniline ring; ii) a conserved hydroxy group on the salicylic ring, and iii) a free amide group in the middle have cytotoxic activity. Further work will be completed using western blot to determine if there’s any correlation between androgen receptor degradation and in vitro potency. In conclusion, Niclosamide analogs have indicated promising potential to inhibit HCC cell lines by targeting the Androgen Receptor. Citation Format: Jeffrey Cheng, Enming Xing, Shabber Mohammed, Emma Montgomery, Lauren Granchie, Christopher Coss, Pui-Kai Li. Design, synthesis, and screening of niclosamide analogs as androgen receptor degraders for hepatocellular carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3106.